My 4-year old Motorguide has developed an issue where, when running at the highest speed setting (5), it will go for a couple of minutes then cut out. I can dial it down to 3 or 4 and it will run all day. Often I can crank it back up and get another couple minutes. 
 

I do have an inline breaker and it is not tripping. I run two 12v batteries rigged in parallel for longer run time. 
 

Any ideas?

Seems like a battery load issue, maybe try using them under full load individually and see if one cuts out.

If they are lithium batteries then you are exceeding the long term current limit set in the BMS.  If they are not lithium batteries,  I have no clue.

Does it have a overload system? Maybe thermal  or amperage overload in the motor electronics? Might check the prop and make sure you don't have a wad of line around the shaft.  The other thing to check would be to check your electrical connections.

Good luck,

FM

4 hours ago, Tennessee Boy said:

If they are lithium batteries then you are exceeding the long term current limit set in the BMS.  If they are not lithium batteries,  I have no clue.

Not lithium.